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Questions tagged [vegdist]

10 questions
3
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1 answer

R metaMDS ordination distances

I have been doing some ordinations on a data set that I have of abundances of species at different sampling points. I am using metaMDS() in vegan to do this. With this function you can either: enter directly the community data (sites in rows and…
Caitlyn_D
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2 answers

Error when performing an NMDS in R using package vegdist

I'm trying to perform an NMDS in R using the vegan package on a data set that has plots as columns and species counts as columns. My data is in the format of a text file (tab delimited) and contains a lot of '0' species counts. However, when I try…
user1182741
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1 answer

calculating bray curtis dissimilarity between each treatment to control within each group

I need to calculate bray curtis dissimilarity of two treatments to a control. but this is nested by site. if I use the entire dataframe, the bray curtis dissmilarity takes into account distances between sites, which I need to avoid. below is a mock…
Felipe Albornoz
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Bray–Curtis distance calculation method in Complexheatmap?

I'm using the Complexheatmap function (or "Heatmap") in R and was wondering if there was a way to use the Bray-Curtis method in calculating col/row distance (with ward.D2 clustering method) since it's not a supported method in Complexheatmap. I need…
Nate
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How do I use the adonis3 function in the GUniFrac package?

I am stuck on trying to use the adonis3 and dmanova functions in the GUniFrac package in R. I am having trouble getting my feature table and distance matrix in the right format for the LHS part of the formula. I import both tables into R with…
Sterling Wright
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Which distance matrix to compute on my absence/presence dataset with many zeros?

I am doing analyses on a dataset of parasite species present or absent in bee samples. I have a matrix with 0/1 for each sample and each parasite species. Since a lot of samples do not have any parasite species, a lot of the rows are all zeroes. I…
Tina Tuerlings
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how to preform a PCoA with constraind factors

I have performed the following PCoA, using the following code: spe.dist <- vegdist(spe, method = "bray") spe.braysq.pcoa <- pcoa(sqrt(spe.dist)) biplot.pcoa(spe.braysq.pcoa, sqrt(spe)) However, I now want to perform a constrained PCoA. I want…
Herbuiten
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How to split vegdist matrices according to geographic distance to perform Mantel or MRM analysis?

I am using vegan Mantel and partial Mantel tests to infer the correlation between those two matrices. Since I have distance ranging from 0 to 400 km, I want to split those matrices in two groups: Mantel comparing A and B from 0 to 114 km (threshold…
Dennis Göss
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Should I use vegdist or dist for hclust?

I am trying to do a hierarchical cluster analysis with binary data, and for the distance matrix I applied the function vegdist() from vegan package: dist.jac <- vegdist(final_df, method="jaccard", binary = TRUE) Next, I used the function hclust but…
Inês Pereira
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Compute dissimilarity matrix in R

I wanted to compute a dissimilary matrix IN R by using the following code. a <- A[,-c(2,3,4)] b <- a[-c(201:321), ] b <- unlist(b) library(vegan) PD.dist <- vegdist(b, method = "jaccard", binary = TRUE) Pd.dist The software R put the following…
aweman
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